Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for MGAM
Basic gene info.Gene symbolMGAM
Gene namemaltase-glucoamylase (alpha-glucosidase)
SynonymsMG|MGA
CytomapUCSC genome browser: 7q34
Genomic locationchr7 :141695678-141806547
Type of geneprotein-coding
RefGenesNM_004668.2,
Ensembl idENSG00000259858
Descriptionbrush border hydrolasemaltase-glucoamylase, intestinal
Modification date20141211
dbXrefs MIM : 154360
HGNC : HGNC
Ensembl : ENSG00000257335
HPRD : 01104
Vega : OTTHUMG00000158395
ProteinUniProt: O43451
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MGAM
BioGPS: 8972
Gene Expression Atlas: ENSG00000259858
The Human Protein Atlas: ENSG00000259858
PathwayNCI Pathway Interaction Database: MGAM
KEGG: MGAM
REACTOME: MGAM
ConsensusPathDB
Pathway Commons: MGAM
MetabolismMetaCyc: MGAM
HUMANCyc: MGAM
RegulationEnsembl's Regulation: ENSG00000259858
miRBase: chr7 :141,695,678-141,806,547
TargetScan: NM_004668
cisRED: ENSG00000259858
ContextiHOP: MGAM
cancer metabolism search in PubMed: MGAM
UCL Cancer Institute: MGAM
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MGAM in cancer cell metabolism1. Yang S (2007) Gene amplifications at chromosome 7 of the human gastric cancer genome. International journal of molecular medicine 20: 225-231. go to article

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Phenotypic Information for MGAM(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MGAM
Familial Cancer Database: MGAM
* This gene is included in those cancer gene databases.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_GALACTOSE_METABOLISM
KEGG_STARCH_AND_SUCROSE_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 154360; gene.
Orphanet
DiseaseKEGG Disease: MGAM
MedGen: MGAM (Human Medical Genetics with Condition)
ClinVar: MGAM
PhenotypeMGI: MGAM (International Mouse Phenotyping Consortium)
PhenomicDB: MGAM

Mutations for MGAM
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MGAM related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample11   11      2   
GAIN (# sample)11   11      2   
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=37)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr7:141708471-141708471p.R98Q7
chr7:141719069-141719069p.S133F4
chr7:141724872-141724872p.A302V2
chr7:141708362-141708362p.P62S2
chr7:141705382-141705382p.V18F2
chr7:141719039-141719039p.G123E2
chr7:141722220-141722220p.R288K2
chr7:141721447-141721447p.G207E2
chr7:141719073-141719073p.K134N2
chr7:141724852-141724852p.N295N2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample4123297 16 63 45126 48915225
# mutation4123366 17 53 51136 416018244
nonsynonymous SNV482255 14 22 4165 111910130
synonymous SNV 41111 3 31 1071 3418114
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr7:141758086p.R834Q5
chr7:141747587p.P1327P5
chr7:141759688p.I1259I5
chr7:141708471p.R1097C4
chr7:141754683p.R98Q4
chr7:141803141p.F1677F3
chr7:141760126p.T861T3
chr7:141747669p.E1800K3
chr7:141797419p.P1359S3
chr7:141734499p.R1039C2

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for MGAM in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for MGAM

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

AHCYL2,ATP12A,ATP1A4,BMPER,CASQ1,EGF,ESRRG,
FRAS1,HERC1,ESRG,IGFBP2,LOC100128164,LOC374491,LRTM1,
MGAM,MYNN,PPP1R3C,TMC3,TMPRSS7,WDR72,ZNF37BP
ADAM8,APOC1,CELA1,CHIT1,DEC1,DNAJC5B,HOXB9,
HS3ST2,HTRA4,LILRA4,MGAM,LINC00112,NKX2-6,OR11A1,
PKD2L1,PRAMEF22,SCARNA11,SDS,SNORA27,SULT1E1,TNFRSF11B

AJAP1,ARG1,AVPR1A,CLEC4D,COL15A1,CXCR1,CXCR2,
SUPT20HL2,FPR1,FPR2,GPR97,HRH2,IL7R,LINGO4,
MGAM,PADI4,PGLYRP1,S100A12,SELE,TCTE1,TNC
AADAC,ALDOB,APOA1,APOA4,APOB,APOC3,C17orf78,
ERICH4,CEACAM20,CRISP1,DPEP1,ENPEP,FABP6,GSTA2,
GSTA5,KCNJ13,LOC285733,MGAM,ONECUT3,SLC2A2,SLC5A12,
SL
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for MGAM
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB O43451; -.
ChemistryChEMBL CHEMBL2074; -.
ChemistryGuidetoPHARMACOLOGY 2627; -.
Organism-specific databasesPharmGKB PA30778; -.
Organism-specific databasesCTD 8972; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00284maltase-glucoamylase (alpha-glucosidase)approved; investigationalAcarbose
DB00491maltase-glucoamylase (alpha-glucosidase)approvedMiglitol
DB04878maltase-glucoamylase (alpha-glucosidase)approved; investigationalVoglibose
DB04465maltase-glucoamylase (alpha-glucosidase)experimentalLactose


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Cross referenced IDs for MGAM
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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